Local calculations were added for EDcalculator.Extended alphabets (-alphabet flag) added to Rsample.nucleotides in addition to A, C, G, U/T). Added the capability to design to use extended alphabets (i.e.Biased selection of loop nucleotides and helix base pairs added to design.

Improved the documentation about data tables.

Added the command line program SymmetryTester, which checks for proper symmetries in data tables.

Use M or 6 to represent m6A in sequences.

These can be accessed using -alphabet m6A in most command line programs. Added the m6A nearest neighbor parameters.Files were in dos text, and the dangling end free energies were not being correctly read on Linux. Fixed a problem with m6A thermodynamic parameter files.This enables it to work on sequences with extended alphabets. Revised scorer so that it ignores nucleotide identities.Added -alphabet option to use alternative folding alphabets to AllSub, bifold, bipartition, and DuplexFold.Added a new -stemloop option to calculate hairpin stemloop probabilities to ProbScan.

Run-Command 6.01 free